User: Dattatray Mongad
Dattatray Mongad • 240
- Reputation:
- 240
- Status:
- Trusted
- Location:
- National Centre for Cell Science, Pune
- Website:
- http://www.nccs.res.in/
- Twitter:
- DattatrayMongad
- Last seen:
- 4 days ago
- Joined:
- 2 years, 5 months ago
- Email:
- d************@gmail.com
Posts by Dattatray Mongad
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... Yes you can do PCA using TPM values and TMM has been widely used as normalization technique for transcriptome data.
You can use [DESeq2][1]
[1]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html ...
written 4 days ago by
Dattatray Mongad • 240
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... **use biopython:**
from Bio import SeqIO
for records in SeqIO.Parse("fastaFileName","fasta"):
print( records.id )
print( records.seq ) ...
written 12 weeks ago by
Dattatray Mongad • 240
• updated
12 weeks ago by
h.mon ♦ 23k
1
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... In simple words, your idea is to take APOE gene sequence and blast it against genomes of other organisms. Using some strict BLAST output cutoffs you will manage to get estimated copy numbers of gene but not the expression levels. For measuring expression you will need microarray or transcriptome or ...
written 12 weeks ago by
Dattatray Mongad • 240
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... The server or tool depend on your protein ids. If its UniProt ids, then you can use UniProt id conversion tool and convert them to KEGG ids. Then use KeggMapper to get the list of pathways involved. You can follow typical gene enrichmnet analysis also. ...
written 3 months ago by
Dattatray Mongad • 240
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... Core means, bacterial OTU/genera present in all samples or individuals. To do core microbiome analysis please see this [tutorial][1]
[1]: https://microbiome.github.io/microbiome/Core.html ...
written 3 months ago by
Dattatray Mongad • 240
0
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1
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169
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Answer:
A: Gut microbe annotation DB
... I am assuming you are using amplicon sequencing approach.
Currently, there is not tool or database which can tell you all information at once. Bu you can play around to gather such information.
1. Use [PICRUSt][1], to discover genes present in your data and their abundances (in terms of KO and CO ...
written 3 months ago by
Dattatray Mongad • 240
1
vote
1
answer
346
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Answer:
A: gff3 to gtf conversion
... See previous posts here [45791][1]
[1]: https://www.biostars.org/p/45791/ ...
written 3 months ago by
Dattatray Mongad • 240
1
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2
answers
290
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... See the link [POP][1]. You can also find some references and original scripts to generate the matrix there.
[1]: http://www.drive5.com/pop/VTML200I ...
written 4 months ago by
Dattatray Mongad • 240
3
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2
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290
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... BLOSUM and PAM series matrices are available on NCBI ftp.
See this link: ftp://ftp.ncbi.nih.gov/blast/matrices/ ...
written 4 months ago by
Dattatray Mongad • 240
0
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... use this [Python script][1]. Easy to use: python contigPlot.py fastaDir.
Where fastaDir is directory name containing genome files (extension .fasta)
[1]: https://github.com/drdee255/code-Util/blob/master/contigPlot.py ...
written 4 months ago by
Dattatray Mongad • 240
Latest awards to Dattatray Mongad
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: Amino Acid matrices freely downloadable url
Scholar
3 months ago,
created an answer that has been accepted.
For A: Amino Acid matrices freely downloadable url
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Amino Acid matrices freely downloadable url
Scholar
6 months ago,
created an answer that has been accepted.
For A: Extract specific fasta sequences from multiple multi-fasta files located in a di
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